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ChipSeeker Heatmap (y-axis)?

I was wondering if there is a way to adjust the Y-axis on the Heatmap produced through Chipseeker. I am pulling down a transcription factor with and without its inhibitor. As expected, there are considerably less peaks in the heatmap, however, they are spread out along the same Y-axis and therefore visually inaccurate. The image is linked below!

thanks!

peaks Peak1 is Control and Peak2 is treated.

chip-seq chipseeker
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updated by Rashedul Islam Rashedul Islam • written by dthaper • dthaper

What is the center of the heatmap? Can you rephrase your question?

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written by Rashedul Islam Rashedul Islam

The center of the heatmap is transcription start sites. Peaks in the middle is binding at the TSS. Peak 1 has over 10,000 binding sites while Peak 2 has around 700. But since the Y-axis is the same, Peak 2 looks like it has more binding to an un-trained eye. Its hard to present the data this way.

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written by dthaper • dthaper

2 answers

anyone able to help with this?

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written by dthaper • dthaper

They are spread because you plotter around the TSS. To see the difference you are expecting, plot the binding sites around the peak centers of peak1 instead of TSS.

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written by Rashedul Islam Rashedul Islam

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